NM_001142782.2:c.316+15482C>A

Variant names:

• chr1-113406831-C-A
• rs11102625
• NM_001142782.2:c.316+15482C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142782.2(MAGI3):​c.316+15482C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,004 control chromosomes in the GnomAD database, including 21,627 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21627 hom., cov: 32)
• Consequence: MAGI3 NM_001142782.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 5 publications found

Genes affected

MAGI3 (HGNC:29647): (membrane associated guanylate kinase, WW and PDZ domain containing 3) Predicted to enable frizzled binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within positive regulation of JUN kinase activity. Located in cell junction. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGI3	NM_001142782.2	c.316+15482C>A		intron_variant	Intron 1 of 20	ENST00000307546.14	NP_001136254.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGI3	ENST00000307546.14	c.316+15482C>A		intron_variant	Intron 1 of 20	5	NM_001142782.2	ENSP00000304604.9

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79360 AN: 151886 Hom.: 21608 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.473

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.522 AC: 79420 AN: 152004 Hom.: 21627 Cov.: 32 AF XY: 0.517 AC XY: 38441 AN XY: 74284

African (AFR) AF: 0.644 AC: 26681 AN: 41444

American (AMR) AF: 0.467 AC: 7123 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1650 AN: 3472

East Asian (EAS) AF: 0.184 AC: 951 AN: 5178

South Asian (SAS) AF: 0.599 AC: 2884 AN: 4818

European-Finnish (FIN) AF: 0.420 AC: 4437 AN: 10556

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33954 AN: 67974

Other (OTH) AF: 0.472 AC: 995 AN: 2106

Alfa AF: 0.505 Hom.: 21322

Bravo AF: 0.524

Asia WGS AF: 0.433 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.56
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11102625; hg19: chr1-113949453;